Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli. - Osbaldo Resendis-Antonio; Jennifer L. Reed; Sergio Encarnación; Julio Collado-Vides; Bernhard Ø. Palsson (PLoS Comput. Biol., 2007)

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. - Anu Raghunathan; Jennifer L. Reed; Sook-Il Shin; Bernhard Ø. Palsson; Simon Daefler (BMC Syst. Biol., 2009)

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. - Joonhoon Kim; Jennifer L. Reed (BMC Syst. Biol., 2010)

An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models. - Dipak Barua; Joonhoon Kim; Jennifer L. Reed (PLoS Comput. Biol., 2010)

Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation. - Grigoriy E. Pinchuk; Eric A. Hill; Oleg V. Geydebrekht; Jessica De Ingeniis; Xiaolin Zhang 004; Andrei Osterman; James H. Scott; Samantha B. Reed; Margaret F. Romine; Allan E. Konopka; Alexander S. Beliaev; Jim K. Fredrickson; et al. (PLoS Comput. Biol., 2010)

The evolution of metabolic networks of E. coli. - David J. Baumler; Roman G. Peplinski; Jennifer L. Reed; Jeremy D. Glasner; Nicole T. Perna (BMC Syst. Biol., 2011)

iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. - Saheed Imam; Safak Yilmaz; Ugur Sohmen; Alexander S. Gorzalski; Jennifer L. Reed; Daniel R. Noguera; Timothy J. Donohue (BMC Syst. Biol., 2011)

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. - Ines Thiele; Daniel R. Hyduke; Benjamin Steeb; Guy Fankam; Douglas K. Allen; Susanna Bazzani; Pep Charusanti; Feng-Chi Chen; Ronan M. T. Fleming; Chao A. Hsiung; Sigrid C. J. De Keersmaecker; Yu-Chieh Liao; et al. (BMC Syst. Biol., 2011)

Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. - Jan Schellenberger; Daniel C. Zielinski; Wing Choi; Sunthosh Madireddi; Vasiliy Portnoy; David A. Scott; Jennifer L. Reed; Andrei Osterman; Bernhard Ø. Palsson (BMC Syst. Biol., 2012)

Shrinking the Metabolic Solution Space Using Experimental Datasets. - Jennifer L. Reed (PLoS Comput. Biol., 2012)

Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142. - Trang T. Vu; Sergey M. Stolyar; Grigoriy E. Pinchuk; Eric A. Hill; Leo A. Kucek; Roslyn N. Brown; Mary S. Lipton; Andrei Osterman; Jim K. Fredrickson; Allan E. Konopka; Alexander S. Beliaev; Jennifer L. Reed (PLoS Comput. Biol., 2012)

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models. - Cameron Cotten; Jennifer L. Reed (BMC Bioinform., 2013)

Inferring ancient metabolism using ancestral core metabolic models of enterobacteria. - David J. Baumler; Bing Ma; Jennifer L. Reed; Nicole T. Perna (BMC Syst. Biol., 2013)

Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. - Wai Ong; Trang T. Vu; Klaus N. Lovendahl; Jenna M. Llull; Margrethe H. Serres; Margaret F. Romine; Jennifer L. Reed (BMC Syst. Biol., 2014)

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community. - Joshua J. Hamilton; Montserrat Calixto Contreras; Jennifer L. Reed (PLoS Comput. Biol., 2015)

Improving flux predictions by integrating data from multiple strains. - Matthew R. Long; Jennifer L. Reed (Bioinform., 2017)

Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis. - Mingyuan Tian; Jennifer L. Reed (Bioinform., 2018)

Workflow Analysis Driven Recommendations for Integration of Electronically-Enhanced Sexually Transmitted Infection Screening Tools in Pediatric Emergency Departments. - Jessica L. Howe; Jennifer L. Reed; Katharine T. Adams; Cara Elsholz; Erin M. Augustine; Andrea T. Cruz; Cynthia Mollen; Michelle L. Pickett; Sara Schmidt; Kristin Stukus; Raj M. Ratwani; Monika K. Goyal (J. Medical Syst., 2020)

Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4. - Wai Kit Ong; Dylan K. Courtney; Shu Pan; Ramon Bonela Andrade; Patricia J. Kiley; Brian F. Pfleger; Jennifer L. Reed (PLoS Comput. Biol., 2020)